The underlying MVA solver is working fine. MVA does not compute the average over all classes directly. Disk B does not see the system throughput. It only sees throughput from two classes. Since the average response time is computed using the throughput result, the value is too high (Disk B only sees a fraction of the total throughput).
I have attached the full output from qnap2. It includes the source code for qnap2. The output above is for Beta=1..5. Here is the output from JMVA for Disk B with Beta=5. The per-class results match (though qnap2 uses real*4). System response time is a derived value. <stationresults station="Disk B"> <classresults customerclass="OE"> <measure meanValue="0.6589864605709487" measureType="Number of Customers" successful="true"/> <measure meanValue="1.5954233130406923" measureType="Throughput" successful="true"/>...
Aggregate residence time/response time incorrect for station with zero visits